I'm not sure what you mean by "emptying", but my suspicion is that you cleaned your document partition. There was no need to do that in the first place and it likely won't help. As described above, probably your settings partition is full. How that happened is still open for speculation, but yes, it can happen. But you cannot access it via USB mass storage, and I'm not sure if I should really suggest USB networking since that requires you to know very well what you are doing with the shell access.
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